Clear the Coast program manager Wil Soltau says the six-metre skiff was spotted during the program's first fly-by of the north and west coasts of Vancouver Island.
The program, which is run by the Living Oceans Society, has been working with West Coast Helicopters to patrol remote areas of the coast.
Soltau says he's seen a lot of debris believed to be from Japan, but the discovery of the fiberglass skiff along with several life jackets was emotional nevertheless.
"You know, you think about the event itself, the people that were affected by it, the people who lost their lives and their homes," Soltau told CBC News.
Now it's up to Transport Canada to try to identify the vessel and decide whether it has invasive species or is a danger to the marine environment.
However, Soltau says the new boat may not be at the same spot where it was found two weeks ago.
"It's on the west coast of Vancouver Island at a location that is a high energy wave action spot and we did have some pretty bad weather last week so I'm kind of doubtful whether the boat is still in the same location where we saw it."
Soltau says a similar vessel was found on Spring Island near Kyuquot last August. A much larger 50-metre vessel was also sunk by the U.S. Coast Guard off the west coast of Alaska last April.
The tsunami was generated after a magnitude 9.0 earthquake struck off the coast of northern Japan in March 2011.
The huge waves and swells of the tsunami moved inland and then retreated back into the Pacific Ocean, carrying with them the wreckage of buildings, cars and boats. Nearly 19,000 people were killed.